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Archive for the ‘PubMed’ Category

PMC Citation Exporter Feature Now Available!

PMC (PubMed Central) is happy to announce the addition of a citation exporter feature. This feature makes it easy to retrieve either styled citations that you can copy/paste into your manuscripts, or to download them into a format compatible with your bibliographic reference manager software.

When viewing a search results page, each result summary will now include a “Citation” link. When, clicked, this will open a pop-up window that you can use to easily copy/paste citations formatted in one of three popular styles: AMA (American Medical Association), MLA (Modern Library Association, or APA (American Psychological Association). In addition, the box has links at the bottom that can be used to download the citation information in one of three machine-readable formats, which most bibliographic reference management software can import. The same citation box can also be invoked from an individual article, either in classic view (with the “Citation” link among the list of formats) or the PubReader view, by clicking on the citation information just below the article title in the banner.

Citation Exporter Feature screenshot

These human-readable styled citations, and machine-readable formats, will be available through a public API. Further details will be provided in another announcement, on the pmc-utils-announce mailing list. Please subscribe to that list if you are interested in updates.

MeSH Browser Now Updated More Frequently

Beginning on September 4, 2014, the MeSH Browser is being updated each business day. The MeSH XML and ASCII format files for Supplementary Concept Records (SCRs) will be available on this same Monday through Friday schedule starting the week of September 15, 2014. Prior to this change, the MeSH Browser and MeSH XML and ASCII files for SCRs were updated and made available once per week.

This new update schedule releases new and edited SCRs, mostly for chemicals and drugs, in a more timely way for use by both indexers and searchers. Descriptors and qualifiers are changed only on an annual basis.

2015 Medical Subject Headings (MeSH) Now Available!

MeSH Vocabulary Changes for 2015 is now available! Lists of new descriptors, changed descriptors, deleted descriptors, and new descriptors by tree subcategory are available on the NLM website. For more information about MeSH use and structure, as well as recent updates and availability of data, visit the updated Introduction to MeSH – 2015 webpage.

Note: The default year in the MeSH Browser remains 2014 MeSH for now, but the alternate link provides access to 2015 MeSH. The MeSH Section will continue to provide access via the MeSH Browser for two years of the vocabulary; the current year and an alternate year. Sometime in November or December, the default year will change to 2015 MeSH and the alternate link will provide access to the 2014 MeSH.

Population Health Added to Special Queries

The NLM PubMed Special Queries page includes a link to a new MEDLINE/PubMed Population Health search. A definition for population health is “the health outcomes of a group of individuals, including the distribution of such outcomes within the group. The field of population health includes health outcomes, patterns of health determinants, and policies and interventions that link these to differences between groups of people.” 1

The Population Health Special Query is a PubMed search of relevant MeSH headings and text words combined strategically to retrieve PubMed citations. MeSH headings were selected with the assistance of members of the Institute of Medicine Board on Population Health and Public Health.

1 Kindig D, Stoddart G. What is population health? Am J Public Health. 2003 Mar;93(3):380-3. PubMed PMID: 12604476.

MeSH on Demand Update: How to Find Citations Related to Your Text

Screenshot of the MeSH on Demand results pageIn May 2014, NLM introduced MeSH on Demand, a Web-based tool that suggests MeSH terms from your text such as an abstract or grant summary up to 10,000 characters using the MTI (Medical Text Indexer) software. For more background information, see the NLM Technical Bulletin, MeSH on Demand Tool: An Easy Way to Identify Relevant MeSH Terms.

The MeSH on Demand results page is now organized into three sections:

  • Section 1: Original input text (with the length of the input text)
  • Section 2: MeSH terms with links to the MeSH Browser
  • Section 3: Top ten PubMed/MEDLINE citations related to your text

The new MeSH on Demand feature displays the PubMed ID (PMID) for the top ten related citations in PubMed that were also used in computing the MeSH term recommendations. To access this new feature, start from the MeSH on Demand homepage, add your text, such as a project summary, into the box labeled “Text to be Processed.” Then, click the “Find MeSH Terms” button. MeSH on Demand lists the top ten related citation PMIDs from PubMed/MEDLINE. Each PMID is hyperlinked to that citation in PubMed. This new feature in MeSH on Demand is a result of user feedback received from our initial MeSH on Demand release. Users are encouraged to continue to send questions, suggestions, and comments to:

PubMed Commons Update

@PubMedCommonsPubMed Commons set the stage for commenting on any publication in PubMed, the world’s largest searchable database of biomedical literature. New infrastructure and design enhancements have been implemented to improve the user experience and support the PubMed Commons community, and they are now live on PubMed and PubMed Commons. At center stage is new artwork that has been adopted for the PubMed Commons blog, Twitter account, and homepage, to present a clear, unified identity across platforms. The homepage has also been streamlined to consolidate information about joining and using PubMed Commons in a single page to help users get started. A synopsis of the most recent blog post is now available at the top of the homepage to help users stay up-to-date on PubMed Commons.

For several months, comment rating has given members the chance to weigh in on what comments they find useful. Visitors to PubMed can see these ratings alongside comments. Ratings are a key element in calculating the comment and commenter scores that determine the appearance of comments in the “Selected comments” stream on the homepage. Some new site modifications will highlight contributions to PubMed Commons. On the homepage, “Top comments now” will feature the top three recent comments. On PubMed records, “Selected comments” (from the homepage stream) prompt the appearance of an icon above abstracts, directing readers to comments below. And now the most recent tweet about a PubMed Commons comment appears on the homepage for PubMed searches. Check it out!

Share PubMed Abstracts on Facebook, Twitter, and Google+

​Social media icons have been added to the PubMed Abstract display! Click the icon to easily share the PubMed abstract on Facebook, Twitter, and Google+!

Timing and completeness of trial results posted at and published in journals.

NLM to Update MEDLINE/PubMed Daily!

Beginning June 2, 2014, the National Library of Medicine will add new and updated citations to PubMed seven days a week. Daily updating is a welcome enhancement to PubMed. Prior to this change, NLM updated PubMed five times a week on Tuesday through Saturday.

Likewise, new MEDLINE/PubMed update files for NLM data licensees will appear on the ftp server daily by noon ET. More than one update file may become available on the same day. The update files are available all hours seven days per week throughout the year.

For more information, visit the NLM Technical Bulletin.

MLA Theater Presentations Available!

The NLM theater presentation recordings are available from the NLM Web site and have been announced in the NLM Technical Bulletin. The Technical Bulletin article lists the topics. Besides the usual PubMed Update, there are The ACA, Hospital Community Benefit and Needs Assessment: NLM Resources and NLM Resources Used in Disasters. The recordings are also available from the NLM Distance Education Resources page.

Lori Tagawa and Kay Deeney were available for the Using the Results Database presentation because the speaker hadn’t been able to attend MLA. We answered questions from the audience!

MeSH on Demand Tool: An Easy Way to Identify Relevant MeSH Terms

The National Library of Medicine is pleased to announce the launch of MeSH on Demand, a new feature that uses the NLM Medical Text Indexer (MTI) to find MeSH terms.

Currently, the MeSH Browser allows for searches of MeSH terms, text-word searches of the Annotation and Scope Note, and searches of various fields for chemicals. These searches assume that users are familiar with MeSH terms and using the MeSH Browser. Wouldn’t it be great if you could find MeSH terms directly from your text such as an abstract or grant summary? MeSH on Demand has been developed in close collaboration among MeSH Section, NLM Index Section, and the Lister Hill National Center for Biomedical Communications to address this need.

Use MeSH on Demand to find MeSH terms relevant to your text up to 10,000 characters. One of the strengths of MeSH on Demand is its ease of use without any prior knowledge of the MeSH vocabulary and without any downloads. From the MeSH on Demand homepage, add your text, such as an abstract, into the box labeled “Text to be Processed.” Then, click the “Find MeSH Terms” button. Please read the Helpful Hints section of the homepage to improve your results.

For example, the abstract below contains the phrase “treatment-resistant depression.” The relevant MeSH Heading found for that concept is Depressive Disorder, Treatment-Resistant. MeSH on Demand finds MeSH Headings, Publication Types, and Supplementary Concepts, but not Qualifiers (Subheadings). Select the green question mark button next to the MeSH term or the MeSH term itself to open a new window with the MeSH Browser for that MeSH term.

The MeSH on Demand results page

Please note the Disclaimer that these MeSH terms are machine generated by MTI and do not reflect any human review. While the results will be different from human-generated indexing, MeSH on Demand does find relevant MeSH terms that can help jump-start finding MeSH terms in your search area. NLM welcomes your feedback on MeSH on Demand and MTI. Please send comments and questions to NLM Customer Service with “MeSH on Demand” in the subject box. NLM also looks forward to seeing your ideas for other helpful tools to utilize the MeSH vocabulary and NLM resources more easily. Please contact NLM at